Re: [Gmod-schema] GFF bulk loader - fail

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FYI, I think that script  / schema comes from the original schema data that Eric provided as well and was integrated by Deepak. 

Nathan

> On Oct 28, 2016, at 2:15 PM, Shane McCoy <sha...@gm...> wrote:
> 
> Hello!
> I resolved the gff bulk loader issue. 
> I patched the Adapter.pm file like Scott explained and used this script (packaged in Apollo 2.0.4) to upload the schema/ontologies: 
> scripts/load_chado_schema.sh -u username -d apollo-db -h localhost -p 5432 -r -s scripts/chado-schema-with-ontologies.sql.gz
> 
> Thanks Scott & Eric!
> 
> On Wed, Oct 26, 2016 at 6:01 PM, Shane McCoy <sha...@gm... <mailto:sha...@gm...>> wrote:
> You were right - I accidentally removed the new Adapter.pm. Thanks! Running the script is throwing another error though. It did show the 'unable to find synonym type' error for all 200,000+ lines of this sample gff. I uploaded the ontologies/schema from Eric here <https://github.com/erasche/chado-schema-builder/releases>, 1.31-jenkins93 / chado-1.31.sql.gz. 
> 
> unable to find synonym type in cvterm table at /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 3088, <GEN0> line 202429.
> unable to find synonym type in cvterm table at /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 3088, <GEN0> line 202430.
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: I couldn't find the 'Note' cvterm in the database;
> Did you load the feature property controlled vocabulary?
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /home/bjreadin/src/bioperl-live/Bio/Root/Root.pm:444
> STACK: Bio::GMOD::DB::Adapter::handle_note /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm:3901
> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:974 <http://gmod_bulk_load_gff3.pl:974/>
> -----------------------------------------------------------
> Abnormal termination, trying to clean up...
> Attempting to clean up the loader temp table (so that --recreate_cache
> won't be needed)...
> Trying to remove the run lock (so that --remove_lock won't be needed)...
> Exiting...
> 
> I just ran this and wanted to share - I'll look into the other errors too. 
> Thanks! 
> 
> 
> 
> 
> On Wed, Oct 26, 2016 at 5:39 PM, Scott Cain <sc...@sc... <mailto:sc...@sc...>> wrote:
> (re cc-ing the schema mailing list)
> 
> Hi Shane,
> 
> I think you must not have put the new version of Adapter.pm in /usr/local/share/perl/5.22.1/Bio/GMOD/DB/ because line 498 of that module doesn't mention shift, it's:
> 
>   my $arg = shift; 
> 
> Can you double check that file?
> 
>  Scott
> 
> 
> 
> On Wed, Oct 26, 2016 at 5:22 PM, Shane McCoy <sha...@gm... <mailto:sha...@gm...>> wrote:
> >
> > Hi Scott!
> > Thanks for the information. 
> > I did replace the Adapter.pm file and did a clean restart of chado and still got the error:
> >>
> >> $ gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl/> --noexon --analysis --organism Stripedbass --gfffile SBDraft_Pt5.nodna.gff --dbname apollo-db
> >> Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 498.
> >> Compilation failed in require at /usr/local/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl/> line 13.
> >> BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl/> line 13.
> >
> >
> > Should I setup an earlier version Perl maybe? I used v5.18.2 previously on another server and did not have this issue.  
> > Thanks!
> > Shane M. 
> >
> > On Wed, Oct 26, 2016 at 11:34 AM, Scott Cain <sc...@sc... <mailto:sc...@sc...>> wrote:
> >>
> >> Hi Shane,
> >>
> >> The loader module, lib/Bio/GMOD/DB/Adaptor.pm, is quite old and uses an ugly idiom that I'd rather not talk about but it's use has be deprecated in modern Perl.  I don't have a working instance of Chado I can test with handy (later in the week I could spin something up on AWS, but I don't have time now), but I did commit this to github if you want to try it out:
> >>
> >> https://raw.githubusercontent.com/GMOD/Chado/fix_shift_if_defined/chado/lib/Bio/GMOD/DB/Adapter.pm <https://raw.githubusercontent.com/GMOD/Chado/fix_shift_if_defined/chado/lib/Bio/GMOD/DB/Adapter.pm>
> >>
> >> Just download this and replace the one it's complaining about in  /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm.
> >>
> >> Also, you won't be able to load the Relations Ontology via the make command.  You'll need to download
> >>
> >> http://purl.obolibrary.org/obo/ro/subsets/ro-chado.obo <http://purl.obolibrary.org/obo/ro/subsets/ro-chado.obo>
> >>
> >> and use the commands described in INSTALL.Chado.  In brief:
> >>
> >> $ go2fmt.pl <http://go2fmt.pl/> -p obo_text -w xml /path/to/obofile | \
> >> go-apply-xslt oboxml_to_chadoxml - > obo_text.xml 
> >>
> >> and
> >>
> >> $ stag-storenode.pl <http://stag-storenode.pl/> \
> >> -d 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT' \
> >> --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml
> >>
> >> Depending on how you installed DBIx::DBStag, the ".pl" on stag-storenode.pl <http://stag-storenode.pl/> might have to be removed.
> >>
> >> Good luck!
> >> Scott
> >>
> >>
> >> On Wed, Oct 26, 2016 at 8:57 AM, Shane McCoy <sha...@gm... <mailto:sha...@gm...>> wrote:
> >> >
> >> >
> >> > Hello,
> >> > Using Chado VERSION=1.31
> >> > I am getting this error when using the gmod bulk load for Chado:
> >> >
> >> >> $ gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl/> --noexon --analysis --organism "stripedbass" --gfffile SBDraft_Full.nodna.gff --dbname apollo-db
> >> >> Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 498.
> >> >> Compilation failed in require at /usr/local/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl/> line 13.
> >> >> BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl/> line 13.
> >> >
> >> >
> >> > I have bioperl 1.006925 installed. I did see that the make ontologies fails now,
> >> >>
> >> >> Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4
> >> >> fetching files for Relationship Ontology
> >> >>   +http://www.obofoundry.org/ro/ro.obo <http://www.obofoundry.org/ro/ro.obo>
> >> >>     404 Not Found   (http://www.obofoundry.org/ro/ro.obo <http://www.obofoundry.org/ro/ro.obo>)
> >> >> fetching files for Sequence Ontology
> >> >
> >> >
> >> > I am using the https://cpt.tamu.edu/computer-resources/chado-prebuilt-schema/ <https://cpt.tamu.edu/computer-resources/chado-prebuilt-schema/>  recommended sql for this build.
> >> >
> >> > Any thoughts why this is failing? Thanks!
> >> > Shane M.
> >> >
> >> >
> >> >
> >> >
> >> > ------------------------------------------------------------------------------
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> >> >
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at scottcain dot net
> >> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>)                     216-392-3087 <tel:216-392-3087>
> >> Ontario Institute for Cancer Research
> >
> >
> 
> 
> 
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>)                     216-392-3087 <tel:216-392-3087>
> Ontario Institute for Cancer Research
> 
> 
> ------------------------------------------------------------------------------
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